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dbEST - a public database of "expressed sequence tags"
Summary - April 15, 1994
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This is a regular announcement to indicate the status of dbEST at
GenBank, National Center for Biotechnology Information (NCBI),
National Library of Medicine, National Institutes of Health.
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dbEST is a resource (Nature Genetics 4:332-333; 1993), now in its second
year of operation, that contains data from laboratories producing partial,
"single-pass" cDNA sequences (ESTs or "Expressed Sequence Tags").
Although dbEST sequences are incorporated into the new EST Division of
GenBank (Nucl. Acids Res. 21:2963-2965; 1993), annotation in dbEST is
more comprehensive and includes detailed contact information about the
contributors, genetic map locations (when available), and instructions
on obtaining physical DNA clones from the American Type Culture Collection
and other sources. In addition, NCBI periodically updates putative
homology assignments using the BLAST family of programs (Nature Genetics
6:119-129; 1994).
dbEST data is available in a variety of forms, described below.
Information on the current release is as follows:
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Date: 1994-April-15
Database: dbEST
Database version number: 2.7
Number of public entries: 33,931
Summary by Organism
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Homo sapiens (human): 17539
Arabidopsis thaliana (thale cress): 5052
Caenorhabditis elegans (nematode): 4699
Oryza sativa (rice): 4342
Plasmodium falciparum (malaria parasite): 1104
Zea mays (maize): 412
Mus musculus (mouse): 391
Saccharomyces cerevisiae (baker's yeast): 134
Capra hircus (goat): 108
Pyrococcus furiosus (hyperthermophilic archaeon): 50
Macropus eugenii (tammar wallaby): 36
Gallus gallus+domesticus (chicken): 20
Brassica napus (oilseed rape) 18
Nicotiana tabacum (tobacco) 13
Sus scrofa (pig) 11
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ACCESS TO EST DATA
1) The nucleotide sequences may be searched using the BLAST electronic
mail server. For more information send an e-mail message with the
word "help" in the body of the message to blast at ncbi.nlm.nih.gov.
The TBLASTN program wich takes an amino acid query sequence and
compares it with six-frame translations of dbEST DNA sequences is
particularly useful.
2) Full reports on ESTs, including homology data, can be retrieved from
the dbEST electronic mail server. For more information send an
e-mail message with the word "help" in the body of the message to
est_report at ncbi.nlm.nih.gov
3) EST sequences are included in the new EST division of GenBank (R)
available from NCBI on CD-ROMs and by anonymous ftp. Individual records
may be retrieved using the RETRIEVE electronic mail server. For more
information send an e-mail message with the word "help" in the body of
the message to retrieve at ncbi.nlm.nih.gov
4) EST sequences are also available as a flat file in the FASTA format by
anonymous FTP in the /repository/dbEST directory at ncbi.nlm.nih.gov
5) We are currently implementing WWW/Mosaic access to EST information. See
future postings of this announcement and "NCBI News." (For a free
subscription, send a request along with your name and postal mailing
address to: info at ncbi.nlm.nih.gov)
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GenBank
National Center for Biotechnology Information
Building 38A, Rm 8N-803
National Library of Medicine,
National Institutes of Health
Bethesda, MD, 20894, USA
telephone: +1 (301) 496-2475
fax: +1 (301) 480-9241
e-mail: info at ncbi.nlm.nih.gov
WWW URL: http://www.ncbi.nlm.nih.gov
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